Glaucomys sabrinus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mGlaSab2 159.63 Gbp N/A 74.8 GiB
PacBio HiFi (.bam) mGlaSab2 163.20 Gbp N/A 537.3 GiB
Arima mGlaSab2 259.70 Gbp N/A 139.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mGlaSab2 PacBio HiFi (.fq) 159.63 Gbp N/A 74.8 GiB
PacBio HiFi (.bam) 163.20 Gbp N/A 537.3 GiB
Arima 259.70 Gbp N/A 139.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 17 July 2025.
Assemblies
Individual 2 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 21 October 2025
mGlaSab2.HiC.hap1.20251021.fasta.gz (792.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 162.00 Mbp 2 221.23 Mbp
20 4 142.01 Mbp 3 181.66 Mbp
30 7 119.48 Mbp 5 165.46 Mbp
40 9 108.56 Mbp 7 155.30 Mbp
50 12 86.62 Mbp 9 148.35 Mbp
60 16 83.46 Mbp 11 142.05 Mbp
70 20 54.72 Mbp 13 111.24 Mbp
80 27 33.11 Mbp 16 83.63 Mbp
90 41 11.48 Mbp 21 50.70 Mbp
100 356 10.26 Kbp 262 10.26 Kbp
1.000x 356 3.00 Gbp 262 3.00 Gbp
NG based on genome size .
Individual 2 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 21 October 2025
mGlaSab2.HiC.hap2.20251021.fasta.gz (749.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 160.31 Mbp 2 216.96 Mbp
20 4 148.55 Mbp 3 174.57 Mbp
30 6 109.57 Mbp 5 160.31 Mbp
40 9 96.22 Mbp 6 158.72 Mbp
50 12 85.19 Mbp 8 142.78 Mbp
60 15 84.20 Mbp 10 139.47 Mbp
70 19 58.08 Mbp 13 106.84 Mbp
80 26 35.66 Mbp 16 84.41 Mbp
90 39 11.82 Mbp 19 61.53 Mbp
100 281 11.63 Kbp 188 11.63 Kbp
1.000x 281 2.82 Gbp 188 2.82 Gbp
NG based on genome size .
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 21 October 2025
mGlaSab2.MT.20251021.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mGlaSab2.yml (view)
species: Glaucomys sabrinus
specimem: mGlaSab2
projects:
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
combine_for_curation: true
hap1: s3://genomeark/species/Glaucomys_sabrinus/mGlaSab2/assembly_vgp_HiC_2.0/mGlaSab2.HiC.hap1.20251021.fasta.gz
hap2: s3://genomeark/species/Glaucomys_sabrinus/mGlaSab2/assembly_vgp_HiC_2.0/mGlaSab2.HiC.hap2.20251021.fasta.gz
pretext_hap1: s3://genomeark/species/Glaucomys_sabrinus/mGlaSab2/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/s2/mGlaSab2_hap1__s2_heatmap.pretext
pretext_hap2: s3://genomeark/species/Glaucomys_sabrinus/mGlaSab2/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/s2/mGlaSab2_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Glaucomys_sabrinus/mGlaSab2/assembly_vgp_HiC_2.0/evaluation/merqury/mGlaSab2_png/
pacbio_read_dir: s3://genomeark/species/Glaucomys_sabrinus/mGlaSab2/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Glaucomys_sabrinus/mGlaSab2/genomic_data/arima/
pipeline:
  - hifiasm (0.25.0+galaxy0)
  - yahs (1.2a.2+galaxy3)
  - VGP0 mitoHiFi workflow (v0.2.2)
  - VGP1 genomic profiling workflow (v0.4)
  - VGP4 HiFi HiC assembly workflow (v0.3.12)
  - VGP8 HiC scaffolding workflow (v3.1) with default mapq=10
  - VGP9 decontamination workflow (v1.1) 
  - Pre-curation worklfow (v1.0beta6) with mapq=10
notes: This was a Hifiasm-HiC assembly of mGlaSab2 resulting in two haplotype assemblies. HiC data were generated using the Arima library prep kit, and require trimming the first 5 bp off from the 5' end of both read files. The restriction enzymes used were the Arima v2 kit, so the cutting sites are GATC, GANTC, CTNAG, TTAA.
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.